VMD-L Mailing List

From: Guo Zhi (gzgzgz_at_gmail.com)
Date: Wed Mar 14 2007 - 10:33:57 CDT

Dear all VMD users,
        I wish to redefine the range of my atom index in a pdb file, for eg:

I have the following content
ATOM 1529 N ILE B 91 53.509 -23.326 -34.693 1.00 23.04 N
ATOM 1530 CA ILE B 91 54.267 -24.473 -35.134 1.00 20.75 C
ATOM 1531 C ILE B 91 53.356 -25.676 -35.343 1.00 22.86 C
ATOM 1532 O ILE B 91 52.751 -26.174 -34.399 1.00 22.49 O
ATOM 1533 CB ILE B 91 55.360 -24.798 -34.101 1.00 21.72 C
ATOM 1534 CG1 ILE B 91 56.320 -23.611 -34.003 1.00 22.76 C
ATOM 1535 CG2 ILE B 91 56.110 -26.049 -34.493 1.00 18.95 C
ATOM 1536 CD1 ILE B 91 56.994 -23.459 -32.669 1.00 30.15 C
ATOM 1537 N PRO B 92 53.280 -26.177 -36.591 1.00 24.76 N
ATOM 1538 CA PRO B 92 52.455 -27.327 -36.982 1.00 21.51 C
ATOM 1539 C PRO B 92 52.920 -28.633 -36.336 1.00 22.13 C
ATOM 1540 O PRO B 92 54.034 -28.726 -35.805 1.00 21.13 O
ATOM 1541 CB PRO B 92 52.667 -27.391 -38.500 1.00 24.02 C
ATOM 1542 CG PRO B 92 53.067 -25.991 -38.871 1.00 24.99 C
ATOM 1543 CD PRO B 92 54.001 -25.645 -37.762 1.00 23.84 C
ATOM 1544 N PRO B 93 52.062 -29.662 -36.370 1.00 20.52 N
ATOM 1545 CA PRO B 93 52.388 -30.968 -35.801 1.00 20.91 C
ATOM 1546 C PRO B 93 53.589 -31.576 -36.531 1.00 19.58 C
ATOM 1547 O PRO B 93 53.804 -31.305 -37.706 1.00 21.69 O
ATOM 1548 CB PRO B 93 51.127 -31.783 -36.093 1.00 21.05 C
ATOM 1549 CG PRO B 93 50.058 -30.766 -36.056 1.00 18.50 C
ATOM 1550 CD PRO B 93 50.659 -29.622 -36.816 1.00 18.22 C
ATOM 1551 N HIS B 94 54.402 -32.342 -35.813 1.00 21.95 N
ATOM 1552 CA HIS B 94 55.561 -33.021 -36.395 1.00 21.93 C
ATOM 1553 C HIS B 94 56.477 -32.141 -37.257 1.00 21.03 C
ATOM 1554 O HIS B 94 57.011 -32.601 -38.262 1.00 20.09 O
ATOM 1555 CB HIS B 94 55.070 -34.229 -37.210 1.00 23.61 C
ATOM 1556 CG HIS B 94 54.167 -35.147 -36.441 1.00 27.71 C
ATOM 1557 ND1 HIS B 94 54.641 -36.069 -35.534 1.00 26.74 N
ATOM 1558 CD2 HIS B 94 52.817 -35.261 -36.426 1.00 29.08 C
ATOM 1559 CE1 HIS B 94 53.620 -36.716 -34.990 1.00 27.67 C
ATOM 1560 NE2 HIS B 94 52.507 -36.243 -35.514 1.00 27.83 N

OK, then I save it as another pdb format file, then it becomes

ATOM 1 N ILE B 91 53.509 -23.326 -34.693 1.00 23.04 N
ATOM 2 CA ILE B 91 54.267 -24.473 -35.134 1.00 20.75 C
ATOM 3 C ILE B 91 53.356 -25.676 -35.343 1.00 22.86 C
ATOM 4 O ILE B 91 52.751 -26.174 -34.399 1.00 22.49 O
ATOM 5 CB ILE B 91 55.360 -24.798 -34.101 1.00 21.72 C
ATOM 6 CG1 ILE B 91 56.320 -23.611 -34.003 1.00 22.76 C
ATOM 7 CG2 ILE B 91 56.110 -26.049 -34.493 1.00 18.95 C
ATOM 8 CD1 ILE B 91 56.994 -23.459 -32.669 1.00 30.15 C
ATOM 9 N PRO B 92 53.280 -26.177 -36.591 1.00 24.76 N
ATOM 10 CA PRO B 92 52.455 -27.327 -36.982 1.00 21.51 C
ATOM 11 C PRO B 92 52.920 -28.633 -36.336 1.00 22.13 C
ATOM 12 O PRO B 92 54.034 -28.726 -35.805 1.00 21.13 O
ATOM 13 CB PRO B 92 52.667 -27.391 -38.500 1.00 24.02 C
ATOM 14 CG PRO B 92 53.067 -25.991 -38.871 1.00 24.99 C
ATOM 15 CD PRO B 92 54.001 -25.645 -37.762 1.00 23.84 C
ATOM 16 N PRO B 93 52.062 -29.662 -36.370 1.00 20.52 N
ATOM 17 CA PRO B 93 52.388 -30.968 -35.801 1.00 20.91 C
ATOM 18 C PRO B 93 53.589 -31.576 -36.531 1.00 19.58 C
ATOM 19 O PRO B 93 53.804 -31.305 -37.706 1.00 21.69 O
ATOM 20 CB PRO B 93 51.127 -31.783 -36.093 1.00 21.05 C
ATOM 21 CG PRO B 93 50.058 -30.766 -36.056 1.00 18.50 C
ATOM 22 CD PRO B 93 50.659 -29.622 -36.816 1.00 18.22 C
ATOM 23 N HIS B 94 54.402 -32.342 -35.813 1.00 21.95 N
ATOM 24 CA HIS B 94 55.561 -33.021 -36.395 1.00 21.93 C
ATOM 25 C HIS B 94 56.477 -32.141 -37.257 1.00 21.03 C
ATOM 26 O HIS B 94 57.011 -32.601 -38.262 1.00 20.09 O
ATOM 27 CB HIS B 94 55.070 -34.229 -37.210 1.00 23.61 C
ATOM 28 CG HIS B 94 54.167 -35.147 -36.441 1.00 27.71 C
ATOM 29 ND1 HIS B 94 54.641 -36.069 -35.534 1.00 26.74 N
ATOM 30 CD2 HIS B 94 52.817 -35.261 -36.426 1.00 29.08 C
ATOM 31 CE1 HIS B 94 53.620 -36.716 -34.990 1.00 27.67 C
ATOM 32 NE2 HIS B 94 52.507 -36.243 -35.514 1.00 27.83 N

Yes, most of the other items are fine, but the atom indice are changed
after saving. En...at least I want to preserve the original index (and
to begin with arbitrary number i would like to define will be even
better).
I tried to use the following commands in order to make the atom index
begin with 30

                 set sel [atomselect top all]
                 set sel_index [$sel get index]
                 set my_index {}
                 foreach ele_index $sel_index {
                            lappend my_index [expr $ele_index+30]
                 }
                 $sel set index $my_index

Then VMD tell me that it is not legal to save index...
               "atomsel object: set: data not modifiable: index"
Seems that this property is only readable and not for my purpose...

Anyone could give me some help?

Guo Zhi